Rapid Identification of a Genomic Region Conferring Dwarfism in Rapeseed (Brassica napus L.) YA2016-12

Plant height is a vital agronomic trait for crops, including oilseed crops such as rapeseed (Brassica napus L.). It affects the crop yield, oil content, and lodging resistance in rapeseed. In this study, we investigated a dwarf trait controlled by a semi-dominant allele in rapeseed. A dwarf line, YA2016-12, was crossed with a tall line, G184-189, and an F2 population was established. Forty of the tallest plants and 40 of the shortest plants from the F2 population were selected and two DNA pools (tall and dwarf) were constructed by the bulked segregant analysis (BSA) method. The two DNA pools and two parental DNAs were then re-sequenced. A sliding window analysis was used to calculate the Δ(SNP-index) and discover an association region on chromosome A03 with a length of 12.4 Mb. Within this region, we found 1225 genes, including 811 genes with non-synonymous or frameshift mutations between YA2016-12 and G184-189. Alignment to known plant height-related orthologs in Arabidopsis thaliana, as well as KEGG pathway and gene ontology annotations, was used to identify nine candidate genes (BnaA03g31770D, BnaA03g37960D, BnaA03g24740D, BnaA03g40550D, BnaA03g26120D, BnaA03g35130D, BnaA03g42350D, BnaA03g25610D, and BnaA03g39850D) involved in gibberellin or cytokinin signaling. Identification of the causal gene for this trait, and of genetic markers linked to favorable alleles, has potential utility for marker-assisted selection to breed rapeseed varieties with improved height.